MS39   Click here for help

GtoPdb Ligand ID: 10634

Synonyms: compound 6 [PMID: 31895569]
Compound class: Synthetic organic
Comment: MS39 is a PROTAC (proteolysis targeting chimera). It is a hybrid molecule that simultaneously inhibits EGFR kinase activity and targets EGFR for destruction via ubiquitination and proteasomal degradation [2]. The kinase inhibitor portion of the molecule is derived from the first generation EGFR inhibitor gefitinib and it uses a VHL ligand to engage the E3 ligase system.
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 14
Hydrogen bond donors 4
Rotatable bonds 29
Topological polar surface area 219.69
Molecular weight 1055.49
XLogP 7.78
No. Lipinski's rules broken 3
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES COc1cc2ncnc(c2cc1OCCCN1CCN(CC1)C(=O)CCCCCCCCCC(=O)NC(C(C)(C)C)C(=O)N1CC(CC1C(=O)NCc1ccc(cc1)c1scnc1C)O)Nc1ccc(c(c1)Cl)F
Isomeric SMILES COc1cc2ncnc(c2cc1OCCCN1CCN(CC1)C(=O)CCCCCCCCCC(=O)N[C@@H](C(C)(C)C)C(=O)N1C[C@@H](C[C@H]1C(=O)NCc1ccc(cc1)c1scnc1C)O)Nc1ccc(c(c1)Cl)F
InChI InChI=1S/C55H71ClFN9O7S/c1-36-50(74-35-61-36)38-18-16-37(17-19-38)32-58-53(70)45-29-40(67)33-66(45)54(71)51(55(2,3)4)63-48(68)14-11-9-7-6-8-10-12-15-49(69)65-25-23-64(24-26-65)22-13-27-73-47-30-41-44(31-46(47)72-5)59-34-60-52(41)62-39-20-21-43(57)42(56)28-39/h16-21,28,30-31,34-35,40,45,51,67H,6-15,22-27,29,32-33H2,1-5H3,(H,58,70)(H,63,68)(H,59,60,62)/t40-,45+,51-/m1/s1
InChI Key HLFLODKZIGYHNR-LTEFSYCBSA-N
Bioactivity Comments
In cellular assays MS39 degrades mutant EGFR but spares wild type EGFR [2]. The reason for this discrepancy is currently unknown, but the same finding has been reported for another EGFR PROTAC [1]. The DC50 value for MS39 is 5.0 nM in HCC-827 cells and 3.3 nM in H3255 cells.
Selectivity at catalytic receptors
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
epidermal growth factor receptor Hs Inhibitor Inhibition 8.0 pKd - 2
⤷ pKd 8.0 (Kd 1.1x10-8 M) [2]
Description: Dissociation constant determined for wild type EGFR in a competitive binding assay.